Team:ETH Zurich/Modeling/Download

This page contains all the programming code functions and the data we have used in order to generate our results. You can download each of the fourth section as a stand-alone framework and run in order to reproduce the result or investigate our methodology. Some of them requires third part free software (such as the Cobra Toolbox), you can find the links to download them in the description section. Some of them requires data or models previously developed by other groups but freely accessible, we state where and when these object have been used. All the code is enriched with comments for an easily understanding of functions and computational steps.

Genome Static Analysis

Download file: File:ETHZ-iGEM2008-GenomeStaticAnalysis.zip

Compute: This simulation download the genome annotation of E.Coli K12 MG1655 from GenBank and restriction enzymes informations from REBASE. For each restriction enzyme, calculates the fragments generated by digesting the chromosome of the strain. It calculates statistics on various aspects, such as probability of having an essential gene per fragment.

Output: An array of records, each one containing statistical analysis for one of the restriction enzyme groups. Generates five plots that explain the statistical results.

Softwared needed: MATLAB with BioInformatic Toolbox.

Third part code: use of standard Bioinformatic Toolbox functions.

Files and descriptions:

• convertCuttingSitesIntoGeneNames.m - convert informations on cutting sites for restriction enzymes in file names as Blattner Ids and alphanumeric gene names.
• createAtomicKnockoutsForRestEnzymes.m - construct the structure containing fragment patterns for all the selected restriction enzymes.
• createAtomicKnockoutStruct.m - constructe a structure object containing fragment patterns for one restriction enzyme.
• digestionSimulation.m - perform the digestion of chromosome using all the restriction enzymes.
• genomeStaticAnalysis.m - main function, invoke the digestion procedure and plots the five graphs.
• essentialGenes.mat - list of essential genes (single knockouts are mortal), obtained from source cited in Restriction Enzymes Analysis page.

Author(s): Luca and Georg.

Genome-scale Model

Download file: File:ETHZ-iGEM2008-GenomeScaleModel.zip

Compute: This package contains the code for reproducing Figure 2,3,4,5,6 and the code needed to create Figure 7. The package initially loads the genome of E.coli K12 MG1655 from GeneBank and then construct a data structure of gene infos take from the annotation. It then loads two different genome scale models (included in the zip file) that represent the iAF1260 model thymidine auxotrophic, with an external uptake of thymidine, respectively in minimal and in rich medium. It then perform different simulations based on Flux Balance Analysis, such as test of effect of thymidine feeding at different chromosomal size. For detail please refer to the section page.

Output: The figures reported in the corresponding section.

Softwared needed: MATLAB (The Mathworks) with the Bioinformatics Toolbox, the Cobra ToolBox from Palsson's Group at UCSD.

Third part code: the iAF1260 in-silico organism from Palsson's Group at UCSD.

Files and descriptions:

• genomeScaleModel.m -
• changeModelForDNASize.m -
• convertCuttingSitesIntoGeneNames.m -
• create3DPlots.m -
• createAtomicKnockoutsForRestEnzymes.m -
• createAtomicKnockoutStruct.m -
• createPlotChromSizeVsGrowthRate.m -
• createPlotThymVsGrowthRate.m
• extractGenesInfoFromGenomeAnnotation.m -
• genomeScaleModel.m -
• simGeneGreedyRandomWalk.m -
• modelKnockoutMinMedium.mat - data file containing the iAF1260 genome scale model, thymidine auxotrophic, on minimal medium plus external feeding of thymidine.
• modelKnockoutRichMedium.mat - data file containing the iAF1260 genome scale model, thymidine auxotrophic, on rich medium plus external feeding of thymidine.

Author(s): Luca.

Chemostat Selection

Download file: [[]]

Compute:

Output: Softwared needed: MATLAB

Third part code:

Files and descriptions:

Author(s):

Switch Circuit

Download file: [[]]

Compute:

Output: Softwared needed: MATLAB and SimBiology Toolbox

Third part code:

Files and descriptions:

Author(s):